library(cola)
Data is from https://tcga-data.nci.nih.gov/docs/publications/gbm_exp/.
data = read.table("~/analysis/unifiedScaled.txt",
header = TRUE, row.names = 1, check.names = FALSE)
data = as.matrix(data)
subtype = read.table("~/analysis/TCGA_unified_CORE_ClaNC840.txt",
sep = "\t", header = TRUE, check.names = FALSE, stringsAsFactors = FALSE)
subtype = structure(unlist(subtype[1, -(1:2)]), names = colnames(subtype)[-(1:2)])
data = data[, names(subtype)]
dim(data)
## [1] 11861 173
table(subtype)
## subtype
## Classical Mesenchymal Neural Proneural
## 38 56 26 53
Get all supported top methods and partition methods:
all_top_value_methods()
## [1] "sd" "vc" "MAD" "AAC"
all_partition_methods()
## [1] "hclust" "kmeans" "skmeans" "pam" "mclust" "som"
register_top_value_fun(AAC = function(mat) AAC(t(mat), mc.cores = 4))
Run clustering for all combination of methods in batch:
res = run_all_consensus_partition_methods(data, top_n = c(1000, 2000, 4000), k = 2:6, mc.cores = 4,
known_anno = data.frame(subtype = subtype),
known_col = list(subtype = structure(seq_len(4), names = unique(subtype))))
res_list = readRDS("~/analysis/TCGA_subgroup_p0.8.rds")
res_list
## Top rows are extracted by 'sd, vc, MAD, AAC' methods.
## Subgroups are detected by 'hclust, kmeans, skmeans, pam, mclust, som' method.
## Number of partitions are tried for k = 2, 3, 4, 5, 6
##
## Following methods can be applied to this 'ConsensusPartitionList' object:
## [1] "collect_classes" "collect_plots"
## [3] "get_best_k" "get_class"
## [5] "get_single_run" "get_stat"
## [7] "show" "test_to_known_factors"
## [9] "top_rows_heatmap" "top_rows_overlap"
get_best_k(res_list)
## best_k
## sd:hclust 6
## sd:kmeans 4
## sd:skmeans 3
## sd:pam 2
## sd:mclust 2
## sd:som 5
## vc:hclust 5
## vc:kmeans 2
## vc:skmeans 2
## vc:pam 3
## vc:mclust 2
## vc:som 6
## MAD:hclust 6
## MAD:kmeans 4
## MAD:skmeans 3
## MAD:pam 2
## MAD:mclust 2
## MAD:som 5
## AAC:hclust 3
## AAC:kmeans 2
## AAC:skmeans 2
## AAC:pam 2
## AAC:mclust 4
## AAC:som 2
Collect all plots for a k:
collect_plots(res_list, k = 4, fun = plot_ecdf)
collect_plots(res_list, k = 4, fun = consensus_heatmap)
collect_plots(res_list, k = 4, fun = membership_heatmap)
# collect_plots(res_list, k = 3, fun = get_signatures)
get_stat(res_list, k = 4)
## cophcor PAC mean_silhouette tot_withinss
## sd:skmeans 0.9902906 0.03065622 0.9461292 515908.2
## vc:skmeans 0.8879438 0.21614825 0.5618254 574878.4
## MAD:skmeans 0.9917860 0.04217366 0.9408289 515334.7
## AAC:skmeans 0.9838451 0.04969188 0.9055829 480082.7
## sd:mclust 0.9504076 0.20431452 0.7747583 530099.1
## vc:mclust 0.8740280 0.33580814 0.4834314 578804.4
## MAD:mclust 0.9728579 0.13903732 0.8329616 524471.1
## AAC:mclust 0.9507134 0.20952895 0.7212143 487082.8
## sd:som 0.9134786 0.28883730 0.6241455 519812.2
## vc:som 0.8246908 0.40207343 0.4806463 580457.5
## MAD:som 0.9151461 0.28035670 0.6364929 515681.8
## AAC:som 0.8799678 0.29925462 0.5662937 477219.6
## sd:pam 0.9597767 0.09899116 0.8184894 531469.5
## vc:pam 0.9548823 0.16490125 0.7773808 583282.7
## MAD:pam 0.9617178 0.09382500 0.8261648 527140.2
## AAC:pam 0.9644622 0.08439025 0.8551892 485802.1
## sd:kmeans 0.9874768 0.04465861 0.9148519 514742.7
## vc:kmeans 0.8626394 0.28486387 0.5165131 575378.7
## MAD:kmeans 0.9939087 0.03172691 0.9466794 513463.6
## AAC:kmeans 0.9832365 0.07962207 0.8755590 472618.4
## sd:hclust 0.8902708 0.30583397 0.5901399 520961.7
## vc:hclust 0.8412445 0.37525236 0.5039156 585461.5
## MAD:hclust 0.8718519 0.32276054 0.5544088 522535.7
## AAC:hclust 0.8989310 0.30475330 0.4974731 494902.5
## area_increased
## sd:skmeans 0.1227831
## vc:skmeans 0.1212277
## MAD:skmeans 0.1233362
## AAC:skmeans 0.1490848
## sd:mclust 0.1567642
## vc:mclust 0.3533911
## MAD:mclust 0.1869009
## AAC:mclust 0.1602564
## sd:som 0.1793262
## vc:som 0.2517942
## MAD:som 0.1780210
## AAC:som 0.1317615
## sd:pam 0.1514919
## vc:pam 0.1767540
## MAD:pam 0.1422933
## AAC:pam 0.1378385
## sd:kmeans 0.1329748
## vc:kmeans 0.1152486
## MAD:kmeans 0.1296491
## AAC:kmeans 0.1255296
## sd:hclust 0.1974301
## vc:hclust 0.2258603
## MAD:hclust 0.1638498
## AAC:hclust 0.1462913
collect_classes(res_list, k = 4)
Overlap of top rows in different top methods:
par(mfrow = c(1, 3))
top_rows_overlap(res_list, top_n = 1000)
## Loading required namespace: venneuler
top_rows_overlap(res_list, top_n = 2000)
top_rows_overlap(res_list, top_n = 4000)
Also visualize the correspondance of rankings between different scoreing methods:
top_rows_overlap(res_list, top_n = 1000, type = "correspondance")
Heatmaps for the top rows:
top_rows_heatmap(res_list, top_n = 1000)
Get clustering in a specified combination of top method and partition method:
res = get_single_run(res_list, top_method = "MAD", partition_method = "kmeans")
res
## A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
## top rows (1000, 2000, 4000) are extracted by 'MAD' method.
## subgroups are detected by 'kmeans' method.
## best k for subgroups seems to be 4.
##
## Following methods can be applied to this 'ConsensusPartition' object:
## [1] "collect_classes" "collect_plots"
## [3] "consensus_heatmap" "dimension_reduction"
## [5] "get_best_k" "get_class"
## [7] "get_consensus" "get_membership"
## [9] "get_param" "get_signatures"
## [11] "get_stat" "membership_heatmap"
## [13] "plot_ecdf" "select_partition_number"
## [15] "show" "signature_density"
## [17] "test_to_known_factors"
Collect all plots
collect_plots(res)
plots:
select_partition_number(res)
get_best_k(res)
## [1] 4
consensus_heatmap(res, k = 4)
membership_heatmap(res, k = 4)
# get_signatures(res, k = 4)
Get classifications
get_class(res, k = 4)
## class entropy silhouette
## TCGA-02-0003-01A-01 2 0.26468043 0.8602827
## TCGA-02-0010-01A-01 2 0.00000000 0.9881322
## TCGA-02-0011-01B-01 2 0.02888898 0.9846284
## TCGA-02-0014-01A-01 2 0.00000000 0.9881322
## TCGA-02-0024-01B-01 2 0.00000000 0.9881322
## TCGA-02-0026-01B-01 2 0.00000000 0.9881322
## TCGA-02-0028-01A-01 2 0.00000000 0.9881322
## TCGA-02-0046-01A-01 2 0.02888898 0.9832806
## TCGA-02-0047-01A-01 4 0.02888898 0.9652453
## TCGA-02-0048-01A-01 2 0.07072027 0.9707940
## TCGA-02-0060-01A-01 4 0.17667967 0.9178131
## TCGA-02-0069-01A-01 2 0.00000000 0.9881322
## TCGA-02-0074-01A-01 2 0.00000000 0.9881322
## TCGA-02-0080-01A-01 2 0.02888898 0.9846284
## TCGA-02-0084-01A-03 4 0.13603239 0.9278645
## TCGA-02-0087-01A-01 4 0.25494457 0.8708645
## TCGA-02-0104-01A-01 2 0.00000000 0.9881322
## TCGA-02-0114-01A-01 2 0.00000000 0.9881322
## TCGA-02-0281-01A-01 2 0.00000000 0.9881322
## TCGA-02-0321-01A-01 3 0.36096405 0.7797467
## TCGA-02-0325-01A-01 2 0.11745329 0.9608990
## TCGA-02-0338-01A-01 2 0.00000000 0.9881322
## TCGA-02-0339-01A-01 2 0.00000000 0.9881322
## TCGA-02-0432-01A-02 2 0.02888898 0.9846284
## TCGA-02-0439-01A-01 4 0.00000000 0.9618755
## TCGA-02-0440-01A-01 2 0.00000000 0.9881322
## TCGA-02-0446-01A-01 4 0.02888898 0.9652453
## TCGA-06-0128-01A-01 4 0.26468043 0.8631171
## TCGA-06-0129-01A-01 2 0.00000000 0.9881322
## TCGA-06-0146-01A-01 2 0.02888898 0.9846284
## TCGA-06-0156-01A-01 4 0.02888898 0.9652453
## TCGA-06-0166-01A-01 4 0.02888898 0.9652453
## TCGA-06-0174-01A-01 2 0.00000000 0.9881322
## TCGA-06-0177-01A-01 2 0.00000000 0.9881322
## TCGA-06-0238-01A-02 4 0.47902101 0.3934988
## TCGA-06-0241-01A-02 2 0.00000000 0.9881322
## TCGA-06-0410-01A-01 2 0.00000000 0.9881322
## TCGA-06-0413-01A-01 2 0.00000000 0.9881322
## TCGA-06-0414-01A-01 2 0.00000000 0.9881322
## TCGA-06-0646-01A-01 4 0.02888898 0.9652453
## TCGA-06-0648-01A-01 2 0.00000000 0.9881322
## TCGA-08-0245-01A-01 2 0.00000000 0.9881322
## TCGA-08-0344-01A-01 2 0.00000000 0.9881322
## TCGA-08-0347-01A-01 4 0.02888898 0.9652453
## TCGA-08-0348-01A-01 2 0.37390308 0.7220132
## TCGA-08-0350-01A-01 2 0.02888898 0.9846284
## TCGA-08-0353-01A-01 3 0.02888898 0.9524119
## TCGA-08-0359-01A-01 4 0.00000000 0.9618755
## TCGA-08-0385-01A-01 2 0.00000000 0.9881322
## TCGA-08-0517-01A-01 2 0.00000000 0.9881322
## TCGA-08-0524-01A-01 2 0.00000000 0.9881322
## TCGA-12-0616-01A-01 2 0.00000000 0.9881322
## TCGA-12-0618-01A-01 2 0.00000000 0.9881322
## TCGA-02-0089-01A-01 4 0.02888898 0.9652453
## TCGA-02-0113-01A-01 3 0.39188847 0.7276572
## TCGA-02-0115-01A-01 4 0.02888898 0.9652453
## TCGA-02-0451-01A-01 4 0.02888898 0.9652453
## TCGA-06-0132-01A-02 4 0.02888898 0.9652453
## TCGA-06-0133-01A-02 4 0.02888898 0.9652453
## TCGA-06-0138-01A-02 4 0.02888898 0.9652453
## TCGA-06-0160-01A-01 4 0.17667967 0.9178131
## TCGA-06-0162-01A-01 4 0.02888898 0.9652453
## TCGA-06-0167-01A-01 4 0.17667967 0.9178131
## TCGA-06-0171-01A-02 4 0.02888898 0.9652453
## TCGA-06-0173-01A-01 4 0.02888898 0.9652453
## TCGA-06-0179-01A-02 4 0.02888898 0.9652453
## TCGA-06-0182-01A-01 3 0.39188847 0.7276572
## TCGA-06-0185-01A-01 3 0.39188847 0.7276572
## TCGA-06-0195-01B-01 4 0.07990323 0.9583896
## TCGA-06-0208-01B-01 4 0.02888898 0.9652453
## TCGA-06-0214-01A-02 4 0.02888898 0.9652453
## TCGA-06-0219-01A-01 4 0.02888898 0.9652453
## TCGA-06-0221-01A-01 4 0.18912082 0.9119053
## TCGA-06-0237-01A-02 4 0.02888898 0.9652453
## TCGA-06-0240-01A-02 4 0.00000000 0.9618755
## TCGA-08-0349-01A-01 4 0.02888898 0.9652453
## TCGA-08-0380-01A-01 4 0.02888898 0.9652453
## TCGA-08-0386-01A-01 3 0.41832037 0.6771913
## TCGA-08-0520-01A-01 4 0.34003852 0.7616114
## TCGA-02-0007-01A-01 3 0.34722304 0.7871946
## TCGA-02-0009-01A-01 3 0.02888898 0.9552673
## TCGA-02-0016-01A-01 3 0.02888898 0.9552673
## TCGA-02-0021-01A-01 3 0.02888898 0.9552673
## TCGA-02-0023-01B-01 3 0.02888898 0.9552673
## TCGA-02-0027-01A-01 3 0.08869473 0.9424507
## TCGA-02-0038-01A-01 3 0.49479376 0.2948284
## TCGA-02-0043-01A-01 3 0.02888898 0.9537879
## TCGA-02-0070-01A-01 3 0.02888898 0.9537879
## TCGA-02-0102-01A-01 3 0.02888898 0.9537879
## TCGA-02-0260-01A-03 3 0.05774568 0.9492765
## TCGA-02-0269-01B-01 3 0.05107902 0.9527670
## TCGA-02-0285-01A-01 3 0.02888898 0.9537879
## TCGA-02-0289-01A-01 3 0.02888898 0.9552673
## TCGA-02-0290-01A-01 3 0.02888898 0.9537879
## TCGA-02-0317-01A-01 3 0.05107902 0.9527670
## TCGA-02-0333-01A-02 3 0.05107902 0.9527670
## TCGA-02-0422-01A-01 3 0.02888898 0.9552673
## TCGA-02-0430-01A-01 3 0.02888898 0.9552673
## TCGA-06-0125-01A-01 3 0.02888898 0.9552673
## TCGA-06-0126-01A-01 3 0.02888898 0.9552673
## TCGA-06-0137-01A-03 3 0.02888898 0.9552673
## TCGA-06-0145-01A-04 3 0.02888898 0.9552673
## TCGA-06-0148-01A-01 3 0.02888898 0.9537879
## TCGA-06-0187-01A-01 3 0.02888898 0.9537879
## TCGA-06-0211-01B-01 3 0.02888898 0.9552673
## TCGA-06-0402-01A-01 3 0.02888898 0.9537879
## TCGA-08-0246-01A-01 3 0.02888898 0.9537879
## TCGA-08-0354-01A-01 3 0.02888898 0.9537879
## TCGA-08-0355-01A-01 3 0.02888898 0.9552673
## TCGA-08-0357-01A-01 3 0.02888898 0.9552673
## TCGA-08-0358-01A-01 3 0.05774568 0.9492765
## TCGA-08-0375-01A-01 3 0.02888898 0.9552673
## TCGA-08-0511-01A-01 3 0.02888898 0.9552673
## TCGA-08-0514-01A-01 3 0.02888898 0.9537879
## TCGA-08-0518-01A-01 3 0.02888898 0.9537879
## TCGA-08-0529-01A-02 3 0.02888898 0.9552673
## TCGA-08-0531-01A-01 3 0.02888898 0.9552673
## TCGA-02-0057-01A-01 4 0.05774568 0.9604716
## TCGA-02-0004-01A-01 1 0.02888898 0.9809814
## TCGA-02-0006-01B-01 1 0.34003852 0.8003203
## TCGA-02-0025-01A-01 1 0.02888898 0.9809814
## TCGA-02-0033-01A-01 1 0.02888898 0.9809814
## TCGA-02-0034-01A-01 1 0.02888898 0.9809814
## TCGA-02-0039-01A-01 1 0.07072027 0.9699716
## TCGA-02-0051-01A-01 1 0.02888898 0.9809814
## TCGA-02-0054-01A-01 1 0.34520223 0.8162763
## TCGA-02-0055-01A-01 1 0.02888898 0.9809814
## TCGA-02-0059-01A-01 1 0.02888898 0.9809814
## TCGA-02-0064-01A-01 1 0.00000000 0.9815527
## TCGA-02-0075-01A-01 1 0.00000000 0.9815527
## TCGA-02-0079-01A-03 1 0.00000000 0.9815527
## TCGA-02-0085-01A-01 4 0.02888898 0.9606365
## TCGA-02-0086-01A-01 1 0.00000000 0.9815527
## TCGA-02-0099-01A-01 1 0.32884118 0.8309643
## TCGA-02-0106-01A-01 1 0.02888898 0.9809814
## TCGA-02-0107-01A-01 1 0.00000000 0.9815527
## TCGA-02-0111-01A-01 1 0.00000000 0.9815527
## TCGA-02-0326-01A-01 3 0.05107902 0.9527670
## TCGA-02-0337-01A-01 1 0.17667967 0.9325983
## TCGA-06-0122-01A-01 1 0.00000000 0.9815527
## TCGA-06-0124-01A-01 1 0.00000000 0.9815527
## TCGA-06-0130-01A-01 1 0.02888898 0.9809814
## TCGA-06-0139-01A-01 1 0.02888898 0.9809814
## TCGA-06-0143-01A-01 1 0.00000000 0.9815527
## TCGA-06-0147-01A-01 1 0.02888898 0.9809814
## TCGA-06-0149-01A-05 1 0.07072027 0.9699716
## TCGA-06-0152-01A-02 3 0.05774568 0.9506049
## TCGA-06-0154-01A-02 1 0.00000000 0.9815527
## TCGA-06-0164-01A-01 1 0.00000000 0.9815527
## TCGA-06-0175-01A-01 1 0.20523571 0.9269461
## TCGA-06-0176-01A-03 1 0.02888898 0.9809814
## TCGA-06-0184-01A-01 1 0.17667967 0.9325983
## TCGA-06-0189-01A-05 1 0.02888898 0.9809814
## TCGA-06-0190-01A-01 1 0.00000000 0.9815527
## TCGA-06-0194-01A-01 1 0.00000000 0.9815527
## TCGA-06-0197-01A-02 1 0.02888898 0.9809814
## TCGA-06-0210-01A-01 1 0.00000000 0.9815527
## TCGA-06-0397-01A-01 1 0.02888898 0.9809814
## TCGA-06-0409-01A-02 1 0.00000000 0.9815527
## TCGA-06-0412-01A-01 1 0.00000000 0.9815527
## TCGA-06-0644-01A-02 1 0.02888898 0.9809814
## TCGA-06-0645-01A-01 1 0.00000000 0.9815527
## TCGA-08-0346-01A-01 1 0.00000000 0.9815527
## TCGA-08-0352-01A-01 1 0.00000000 0.9815527
## TCGA-08-0360-01A-01 1 0.00000000 0.9815527
## TCGA-08-0390-01A-01 1 0.07072027 0.9699716
## TCGA-08-0392-01A-01 1 0.02888898 0.9809814
## TCGA-08-0509-01A-01 1 0.00000000 0.9815527
## TCGA-08-0510-01A-01 1 0.00000000 0.9815527
## TCGA-08-0512-01A-01 1 0.02888898 0.9809814
## TCGA-08-0522-01A-01 1 0.02888898 0.9809814
## TCGA-12-0619-01A-01 1 0.00000000 0.9815527
## TCGA-12-0620-01A-01 1 0.17667967 0.9233442
MDS or T-sne plots:
dimension_reduction(res, k = 4)
dimension_reduction(res, k = 4, method = "tsne")
Consistency of classes.
collect_classes(res_list, k = 4)
collect_classes(res)
res = hierarchical_partition(data, top_n = c(1000, 2000, 4000),
known_anno = data.frame(subtype = subtype),
known_col = list(subtype = structure(seq_len(4), names = unique(subtype))))
res = readRDS("~/analysis/TCGA_subgroup_hierarchical_partition.rds")
res
## A 'HierarchicalPartition' object with 'MAD:kmeans' method.
##
## +-- 01, 52 cols
## | |-- 011, 37 cols
## | +-- 010, 15 cols
## +-- 00, 121 cols
## |-- 001, 46 cols
## +-- 000, 75 cols
## |-- 0001, 37 cols
## +-- 0000, 38 cols
## |-- 00001, 16 cols
## +-- 00000, 22 cols
## |-- 000001, 9 cols
## +-- 000000, 13 cols
##
## Following methods can be applied to this 'HierarchicalPartition' object:
## [1] "collect_classes" "get_class" "get_signatures"
## [4] "get_single_run" "show" "test_to_known_factors"
collect_classes(res)
get_class(res)
## TCGA-02-0003-01A-01 TCGA-02-0010-01A-01 TCGA-02-0011-01B-01
## "00001" "000000" "000001"
## TCGA-02-0014-01A-01 TCGA-02-0024-01B-01 TCGA-02-0026-01B-01
## "000000" "000000" "000001"
## TCGA-02-0028-01A-01 TCGA-02-0046-01A-01 TCGA-02-0047-01A-01
## "000000" "00001" "0001"
## TCGA-02-0048-01A-01 TCGA-02-0060-01A-01 TCGA-02-0069-01A-01
## "00001" "0001" "000000"
## TCGA-02-0074-01A-01 TCGA-02-0080-01A-01 TCGA-02-0084-01A-03
## "00001" "000001" "0001"
## TCGA-02-0087-01A-01 TCGA-02-0104-01A-01 TCGA-02-0114-01A-01
## "0001" "000000" "000000"
## TCGA-02-0281-01A-01 TCGA-02-0321-01A-01 TCGA-02-0325-01A-01
## "000000" "001" "000001"
## TCGA-02-0338-01A-01 TCGA-02-0339-01A-01 TCGA-02-0432-01A-02
## "000000" "000000" "000001"
## TCGA-02-0439-01A-01 TCGA-02-0440-01A-01 TCGA-02-0446-01A-01
## "0001" "00001" "0001"
## TCGA-06-0128-01A-01 TCGA-06-0129-01A-01 TCGA-06-0146-01A-01
## "0001" "000001" "000001"
## TCGA-06-0156-01A-01 TCGA-06-0166-01A-01 TCGA-06-0174-01A-01
## "0001" "0001" "00001"
## TCGA-06-0177-01A-01 TCGA-06-0238-01A-02 TCGA-06-0241-01A-02
## "00001" "0001" "00001"
## TCGA-06-0410-01A-01 TCGA-06-0413-01A-01 TCGA-06-0414-01A-01
## "00001" "000000" "00001"
## TCGA-06-0646-01A-01 TCGA-06-0648-01A-01 TCGA-08-0245-01A-01
## "0001" "00001" "00001"
## TCGA-08-0344-01A-01 TCGA-08-0347-01A-01 TCGA-08-0348-01A-01
## "000000" "0001" "00001"
## TCGA-08-0350-01A-01 TCGA-08-0353-01A-01 TCGA-08-0359-01A-01
## "000001" "001" "0001"
## TCGA-08-0385-01A-01 TCGA-08-0517-01A-01 TCGA-08-0524-01A-01
## "000001" "00001" "000000"
## TCGA-12-0616-01A-01 TCGA-12-0618-01A-01 TCGA-02-0089-01A-01
## "00001" "00001" "0001"
## TCGA-02-0113-01A-01 TCGA-02-0115-01A-01 TCGA-02-0451-01A-01
## "001" "0001" "0001"
## TCGA-06-0132-01A-02 TCGA-06-0133-01A-02 TCGA-06-0138-01A-02
## "0001" "0001" "0001"
## TCGA-06-0160-01A-01 TCGA-06-0162-01A-01 TCGA-06-0167-01A-01
## "0001" "0001" "0001"
## TCGA-06-0171-01A-02 TCGA-06-0173-01A-01 TCGA-06-0179-01A-02
## "0001" "0001" "0001"
## TCGA-06-0182-01A-01 TCGA-06-0185-01A-01 TCGA-06-0195-01B-01
## "001" "001" "0001"
## TCGA-06-0208-01B-01 TCGA-06-0214-01A-02 TCGA-06-0219-01A-01
## "0001" "0001" "0001"
## TCGA-06-0221-01A-01 TCGA-06-0237-01A-02 TCGA-06-0240-01A-02
## "0001" "0001" "0001"
## TCGA-08-0349-01A-01 TCGA-08-0380-01A-01 TCGA-08-0386-01A-01
## "0001" "0001" "001"
## TCGA-08-0520-01A-01 TCGA-02-0007-01A-01 TCGA-02-0009-01A-01
## "0001" "001" "001"
## TCGA-02-0016-01A-01 TCGA-02-0021-01A-01 TCGA-02-0023-01B-01
## "001" "001" "001"
## TCGA-02-0027-01A-01 TCGA-02-0038-01A-01 TCGA-02-0043-01A-01
## "001" "001" "001"
## TCGA-02-0070-01A-01 TCGA-02-0102-01A-01 TCGA-02-0260-01A-03
## "001" "001" "001"
## TCGA-02-0269-01B-01 TCGA-02-0285-01A-01 TCGA-02-0289-01A-01
## "001" "001" "001"
## TCGA-02-0290-01A-01 TCGA-02-0317-01A-01 TCGA-02-0333-01A-02
## "001" "001" "001"
## TCGA-02-0422-01A-01 TCGA-02-0430-01A-01 TCGA-06-0125-01A-01
## "001" "001" "001"
## TCGA-06-0126-01A-01 TCGA-06-0137-01A-03 TCGA-06-0145-01A-04
## "001" "001" "001"
## TCGA-06-0148-01A-01 TCGA-06-0187-01A-01 TCGA-06-0211-01B-01
## "001" "001" "001"
## TCGA-06-0402-01A-01 TCGA-08-0246-01A-01 TCGA-08-0354-01A-01
## "001" "001" "001"
## TCGA-08-0355-01A-01 TCGA-08-0357-01A-01 TCGA-08-0358-01A-01
## "001" "001" "001"
## TCGA-08-0375-01A-01 TCGA-08-0511-01A-01 TCGA-08-0514-01A-01
## "001" "001" "001"
## TCGA-08-0518-01A-01 TCGA-08-0529-01A-02 TCGA-08-0531-01A-01
## "001" "001" "001"
## TCGA-02-0057-01A-01 TCGA-02-0004-01A-01 TCGA-02-0006-01B-01
## "0001" "010" "011"
## TCGA-02-0025-01A-01 TCGA-02-0033-01A-01 TCGA-02-0034-01A-01
## "010" "010" "010"
## TCGA-02-0039-01A-01 TCGA-02-0051-01A-01 TCGA-02-0054-01A-01
## "011" "010" "011"
## TCGA-02-0055-01A-01 TCGA-02-0059-01A-01 TCGA-02-0064-01A-01
## "010" "010" "011"
## TCGA-02-0075-01A-01 TCGA-02-0079-01A-03 TCGA-02-0085-01A-01
## "011" "011" "0001"
## TCGA-02-0086-01A-01 TCGA-02-0099-01A-01 TCGA-02-0106-01A-01
## "011" "011" "010"
## TCGA-02-0107-01A-01 TCGA-02-0111-01A-01 TCGA-02-0326-01A-01
## "011" "011" "001"
## TCGA-02-0337-01A-01 TCGA-06-0122-01A-01 TCGA-06-0124-01A-01
## "011" "011" "011"
## TCGA-06-0130-01A-01 TCGA-06-0139-01A-01 TCGA-06-0143-01A-01
## "010" "010" "011"
## TCGA-06-0147-01A-01 TCGA-06-0149-01A-05 TCGA-06-0152-01A-02
## "011" "011" "001"
## TCGA-06-0154-01A-02 TCGA-06-0164-01A-01 TCGA-06-0175-01A-01
## "011" "011" "011"
## TCGA-06-0176-01A-03 TCGA-06-0184-01A-01 TCGA-06-0189-01A-05
## "010" "011" "010"
## TCGA-06-0190-01A-01 TCGA-06-0194-01A-01 TCGA-06-0197-01A-02
## "011" "011" "011"
## TCGA-06-0210-01A-01 TCGA-06-0397-01A-01 TCGA-06-0409-01A-02
## "011" "011" "011"
## TCGA-06-0412-01A-01 TCGA-06-0644-01A-02 TCGA-06-0645-01A-01
## "011" "010" "011"
## TCGA-08-0346-01A-01 TCGA-08-0352-01A-01 TCGA-08-0360-01A-01
## "011" "011" "011"
## TCGA-08-0390-01A-01 TCGA-08-0392-01A-01 TCGA-08-0509-01A-01
## "011" "010" "011"
## TCGA-08-0510-01A-01 TCGA-08-0512-01A-01 TCGA-08-0522-01A-01
## "011" "011" "010"
## TCGA-12-0619-01A-01 TCGA-12-0620-01A-01
## "011" "011"